Identification of an efficient phenanthrene-degrading Pseudarthrobacter sp. L1SW and characterization of its metabolites and catabolic pathway

Phenanthrene, a typical chemical of polycyclic aromatic hydrocarbons (PAHs) pollutants, severely threatens health of wild life and human being. Microbial degradation is effective and environment-friendly for PAH removal, while the phenanthrene-degrading mechanism in Gram-positive bacteria is unclear. In this work, one Gram-positive strain of plant growth-promoting rhizobacteria (PGPR), Pseudarthrobacter sp. L1SW, was isolated and identified with high phenanthrene-degrading efficiency and great stress tolerance. It degraded 96.3% of 500 mg/L phenanthrene in 72 h and kept stable degradation performance with heavy metals (65 mg/L of Zn2+, 5.56 mg/L of Ni2+, and 5.20 mg/L of Cr3+) and surfactant (10 CMC of Tween 80). Strain L1SW degraded phenanthrene mainly through phthalic acid pathway, generating intermediate metabolites including cis-3,4-dihydrophenanthrene-3,4-diol, 1-hydroxy-2-naphthoic acid, and phthalic acid. A novel metabolite (m/z 419.0939) was successfully separated and identified as an end-product of phenanthrene, suggesting a unique metabolic pathway. With the whole genome sequence alignment and comparative genomic analysis, 19 putative genes associated with phenanthrene metabolism in strain L1SW were identified to be distributed in three gene clusters and induced by phenanthrene and its metabolites. These findings advance the phenanthrene-degrading study in Gram-positive bacteria and promote the practical use of PGPR strains in the bioremediation of PAH-contaminated environments.

Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics

Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.

Kinetics of PAH degradation by a new acid-metal-tolerant Trabulsiella isolated from the MGP site soil and identification of its potential to fix nitrogen and solubilize phosphorous

Development of an efficient bioinoculum is considered as an appropriate remedial approach to treat the PAHs-metal mixed contaminated sites. Therefore, we aimed to isolate a degrader able to exert an outstanding PAH catabolic potential with added traits of pH-metal-resistance, N-fix or P-solubilization from a manufactured gas plant site soil. The identified strain (MTS-6) was a first low and high molecular weight (LMW and HMW) PAHs degrading Trabulsiella sp. tolerant to pH 5. MTS-6 completely degraded the model 3 [150mgL(-1) phenanthrene (Phe)], 4 [150mgL(-1) pyrene (Pyr)] and 5 [50mgL(-1) benzo[a]pyrene (BaP)] ring PAHs in 6, 25 and 90 days, respectively. Presence of co-substrate (100mgL(-1) Phe) increased the biodegradation rate constant (k) and decreased the half-life time (t1/2) of HMW PAHs (100mgL(-1) Pyr or 50mgL(-1) BaP). The strain fixed 47μgmL(-1)N and solubilized 58μgmL(-1)P during PAH metabolism and exhibited an EC50 value of 3-4mgL(-1) for Cu, Cd, Pb and Zn. Over 6mgL(-1) metal levels was lethal for the microbe. The identified bacterium (MTS-6) with exceptional multi-functional traits opens the way for its exploitation in the bioremediation of manufactured gas plant sites in a sustainable way by employing bioaugmentation strategy.